Collaborative Research: Deciphering complex phenotypes in bacteria aided by continuous genome shuffling and high throughput analytical technologies

生命系统的一个决定性特征是它们能够适应和进化。这一特性可用于生物技术，以生产具有所需特性和功能的微生物。然而，微生物系统的适应会导致性能的不稳定和损失。最大限度地提高生物技术中微生物系统的性能取决于对适应和进化机制的理解。这远不是一项微不足道的任务；它需要新的知识和方法来研究有机体的基因(基因)和特征(表型)之间的“差距”。这项由NSF奖支持的研究重点是开发与所需复杂表型相关的细胞属性知识库。这样的基础可以用来研究基因型和观察到的表型之间的关系，缩小微生物系统这两种特性之间的差距，并使微生物工程在生物技术和生物医学中得到应用。研究人员将招收高中生和本科生，重点是代表性不足的学生，开展生物技术领域的研究。这个项目的中心假设是存在与感兴趣的表型相关的细胞属性。这一假说是基于初步数据形成的，这些数据表明某些细胞特性与特定环境中微生物的适合性之间存在相关性。建议的目标是：1)开发和鉴定重组熟练的无性别菌株，提高重组频率；2)应用无性别菌株来鉴定与复杂表型相关的细胞特性；以及3)产生对多种环境应激源具有耐受性的菌株。这项工作的结果将阐明所确定的细胞属性如何与表型(例如，对应激源的耐受性)、基因以及连接基因和表型的潜在分子机制相关。这一知识可用于以合理的方式改变细胞特性，以增强对工业相关环境应激源的耐受性。该知识库将为生物技术社区提供促进合理菌株工程的重要资源。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

A defining trait of living systems is that they adapt and evolve. This trait can be used in biotechnology to produce microbes with desired properties and functions. However, adaptation of microbial systems can cause instability and loss of performance. Maximizing the performance of microbial systems in biotechnology rests on understanding the mechanisms of adaptation and evolution. This is far from being a trivial task; it requires new knowledge and methods to investigate the “gap” between an organism's genes (genotype) and characteristics (phenotype). The research supported by this NSF award focuses on the development of a knowledge base of cellular properties associated with desired complex phenotypes. Such a base could be used to study the relationship between genotype and the observed phenotype, to narrow the gap between these two properties of a microbial system, and to enable microbial engineering for applications in biotechnology as well as in biomedicine. The researchers will recruit high school and undergraduate students, with a focus on underrepresented students, to conduct research in the area of biotechnology. The central hypothesis of this project is that there exist cellular properties that are correlated with phenotypes-of-interest. The hypothesis is formed based on preliminary data that show correlations between certain cellular properties and microbial fitness in specific environments. The proposed objectives are: 1) to develop and characterize a recombination-proficient genderless strain of E. coli with increased recombination frequency, 2) to apply the genderless strain to identify cellular properties associated with complex phenotypes, and 3) to generate strains with tolerance to multiple environmental stressors. Results from this work will shed light on how cellular properties identified correlate with phenotypes (e.g. tolerance to stressors), genotype, and on the underlying molecular mechanisms that connect the genotype to the phenotype. This knowledge may be used to modify in a rational manner cellular properties to enhance tolerance to industrially-relevant environmental stressors. The knowledge base will provide an important resource for the biotechnology community to facilitate rational strain engineering.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.